SBC logo Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred

Fetching Q9BZH6 from www.uniprot.org...

The NucPred score for your sequence is 0.38 (see score help below)

   1  MLPYTVNFKVSARTLTGALNAHNKAAVDWGWQGLIAYGCHSLVVVIDSIT    50
  51  AQTLQVLEKHKADVVKVKWARENYHHNIGSPYCLRLASADVNGKIIVWDV   100
 101  AAGVAQCEIQEHAKPIQDVQWLWNQDASRDLLLAIHPPNYIVLWNADTGT   150
 151  KLWKKSYADNILSFSFDPFDPSHLTLLTSEGIVFISDFSPSKPPSGPGKK   200
 201  VYISSPHSSPAHNKLATATGAKKALNKVKILITQEKPSAEFITLNDCLQL   250
 251  AYLPSKRNHMLLLYPREILILDLEVNQTVGVIAIERTGVPFLQVIPCFQR   300
 301  DGLFCLHENGCITLRVRRSYNNIFTTSNEEPDPDPVQELTYDLRSQCDAI   350
 351  RVTKTVRPFSMVCCPVNENAAALVVSDGRVMIWELKSAVCNRNSRNSSSG   400
 401  VSPLYSPVSFCGIPVGVLQNKLPDLSLDNMIGQSAIAGEEHPRGSILREV   450
 451  HLKFLLTGLLSGLPAPQFAIRMCPPLTTKNIKMYQPLLAVGTSNGSVLVY   500
 501  HLTSGLLHKELSIHSCEVKGIEWTSLTSFLSFATSTPNNMGLVRNELQLV   550
 551  DLPTGRSIAFRGERGNDESAIEMIKVSHLKQYLAVVFRDKPLELWDVRTC   600
 601  TLLREMSKNFPTITALEWSPSHNLKSLRKKQLATREAMARQTVVSDTELS   650
 651  IVESSVISLLQEAESKSELSQNISAREHFVFTDIDGQVYHLTVEGNSVKD   700
 701  SARIPPDGSMGSITCIAWKGDTLVLGDMDGNLNFWDLKGRVSRGIPTHRS   750
 751  WVRKIRFAPGKGNQKLIAMYNDGAEVWDTKEVQMVSSLRSGRNVTFRILD   800
 801  VDWCTSDKVILASDDGCIRVLEMSMKSACFRMDEQELTEPVWCPYLLVPR   850
 851  ASLALKAFLLHQPWNGQYSLDISHVDYPENEEIKNLLQEQLNSLSNDIKK   900
 901  LLLDPEFTLLQRCLLVSRLYGDESELHFWTVAAHYLHSLSQEKSASTTAP   950
 951  KEAAPRDKLSNPLDICYDVLCENAYFQKFQLERVNLQEVKRSTYDHTRKC  1000
1001  TDQLLLLGQTDRAVQLLLETSADNQHYYCDSLKACLVTTVTSSGPSQSTI  1050
1051  KLVATNMIANGKLAEGVQLLCLIDKAADACRYLQTYGEWNRAAWLAKVRL  1100
1101  NPEECADVLRRWVDHLCSPQVNQKSKALLVLLSLGCFFSVAETLHSMRYF  1150
1151  DRAALFVEACLKYGAFEVTEDTEKLITAIYADYARSLKNLGFKQGAVLFA  1200
1201  SKAGAAGKDLLNELESPKEEPIEE                            1224

Positively and negatively influencing subsequences are coloured according to the following scale:

(non-nuclear) negative ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| positive (nuclear)

with NucPred



If you find NucPred useful, please cite this paper:
NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022
The authors also look forward to your comments and suggestions.

What does the NucPred score mean?

You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper.

NucPred score threshold Specificity Sensitivity
see above fraction of proteins predicted to be nuclear that actually are nuclear fraction of true nuclear proteins that are predicted (coverage)
0.10 0.45 0.88
0.20 0.52 0.83
0.30 0.57 0.77
0.40 0.63 0.69
0.50 0.70 0.62
0.60 0.71 0.53
0.70 0.81 0.44
0.80 0.84 0.32
0.90 0.88 0.21
1.00 1.00 0.02

Sequences which score >= 0.8 with NucPred and which are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.)

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